MCM-41 has been hydrothermally synthesized using fumed silica (SiO2) and silatrane [Si(TEA)(2)] as silica sources. Pd nanoparticles were successfully impregnated to the mesoporous MCM-41 supports. Soybean oil methyl ester was partially hydrogenated by the Pd/MCM-41-SiO2 and Pd/MCM-41-silatrane catalysts under a mild condition (low temperature and pressure). Both catalysts could rapidly and selectively convert the polyunsaturated fatty acid methyl esters (C18:3 and C18:2) to monounsaturated fatty acid methyl esters (C18:1) at 100 degrees C and 0.4 MPa H-2 within 4 h. The results verified that the Pd/MCM-41-silatrane catalyst with the greater surface of Pd active sites had higher catalytic activity, representing in term of turnover frequency (TOF), in partial hydrogenation than Pd/MCM-41-SiO2 under both C18:2 conversions of 40% and 60%. Even if the lower selectivity toward cis-C18:1 was obtained for the former. In addition to the better stable structure of MCM-41-silatrane support as compared to MCM-41-SiO2 support, silatrane precursor is more favorable to diminish the extent of complete hydrogenation than fumed silica as it provided the lower index. Even though, this silica precursor sues for more synthetic step. Due to the higher oxidative stability of Pd/MCM-41-SiO2, MCM-41-SiO2 support was further studied for the later research. When varying the Pd loadings in 0.5-2 wt.% on MCM-41-SiO2 support, the Pd(2)/MCM-41-SiO2 catalyst gave the highest performance (TOF) whether the complete hydrogenation was concurrently accompanied. Results signify that the nature of the silica source and the Pd concentration modified the surface active sites and size distribution of metallic particles, which determine the catalytic reactivity and selectivity.